GBIF data portal, ECPGR working group (2017-03-16)
2 likes3,563 views
The document discusses the Global Biodiversity Information Facility (GBIF) data portal and its significance in biodiversity research and policy, highlighting data availability and usage statistics across various countries. It outlines the infrastructure provided by GBIF for data publishing and discovery, along with examples of research benefiting from GBIF-mediated data. Additionally, it emphasizes the importance of data citation, licenses, and the services available for data analysis and tracking impact.
![Data publishing guidelines
hrp://www.gbif.org/resources?f[0]=gr_purpose%3A955](https://image.slidesharecdn.com/2017-03-16gbifportalecpgralnarp-170317164450/85/GBIF-data-portal-ECPGR-working-group-2017-03-16-77-320.jpg)
GBIF data portal, ECPGR working group (2017-03-16)
- 1. ECPGR Forage and Barley workshop GBIF data portal Dag Endresen GBIF Norway UiO Natural History Museum in Oslo University of Oslo Malmö, Sweden, March 16th 2017 Slides: CC-BY-4.0, GBIF.no
- 3. Asia (lack of data) Africa (lack of data)
- 4. MAP OF NATIONAL PARTICIPANTS Updated January 2017 participatio Asia (lack of data) Africa (lack of data)
- 5. DATA PUBLISHED THROUGH GBIF.ORG www.gbif.org/analytics/global dataavailabilit
- 6. TOTAL DATA PUBLISHED BY COUNTRY AS OF 15 MARCH 2016 All others BE ES ZA GB NL DE AU FR SE US 1 United States 337,528,963 2 Sweden 61,423,202 3 France 40,469,687 4 Australia 36,435,662 5 United Kingdom 29,635,764 6 Germany 28,480,795 7 Netherlands 26,075,010 8 Norway 24,189,098 9 South Africa 21,045,000 10 Spain 14,323,393 dataavailabilit
- 7. OCCURRENCE RECORDS PUBLISHED DURING 2016 BY COUNTRY All others BE ES DK CO NO ZA NL GB DE US 1 United States 83,774,897 2 Germany 15,837,819 3 United Kingdom 15,217,220 4 Netherlands 13,098,430 5 South Africa 9,630,896 6 Norway 4,519,715 7 Colombia 4,122,621 8 Denmark 4,048,381 9 Spain 3,175,906 10 Belgium 2,366,452 http://www.gbif.org/country dataavailabilit
- 8. GBIF provides a data publishing infrastructure
- 14. POSSIBLE UPGRADED PGR NETWORK MODEL v Each dataset is shared from the holding gene bank. v The National Inventory (NI) endorse all national gene banks for EURISCO. v ECPGR Crop databases can access passport data from EURISCO and additional crop specific data from the gene bank IPT interface. v Standard data sharing tools ensure that the genebank dataset is available to other relevant decentralized thematic, regional or global networks. Illustra9on from the GBIF annual report 2009, page 47. 14
- 15. Use of GBIF- mediated data
- 16. DATA DOWNLOAD REQUESTS BY COUNTRY, 2016 All others IT CN IN ZA GB CO ES BR MX US 1 United States 14,700 2 Mexico 14,053 3 Brazil 7,437 4 Spain 6,443 5 Colombia 5,431 6 United Kingdom 5,195 7 South Africa 3,492 8 India 3,480 9 China 3,046 10 Italy 2,389 dataaccessandus
- 17. 2016 2015 2014 2013 2012 2011 2010 2009 2008 0 125 250 375 500 52 89 148 169 229 249 350 407 428 DATAACCESSANDUSE Peer-reviewed publications using GBIF-mediated data
- 18. PEER-REVIEWED USES, BY COUNTRY AND REGION, 2016 Oceania North America Latin America Europe Asia Africa 1 Total # of papers by country 1 United States 148 2 United Kingdom 61 3 Germany 51 4 Brazil 50 5 Australia 48 6 China 41 6 Mexico 41 8 France 39 9 Spain 31 10 Canada 25 10 South Africa 25 Total # of papers by region 1 Europe 351 2 North America 173 3 Latin America 134 4 Asia 94 5 Africa 58 6 Oceania 54 dataaccessandus 2016
- 19. 2016 SCIENCE REVIEW Annual publication summarizes more than 100 peer-reviewed articles that rely on GBIF-mediated data. Accompanying Sourcebook includes more than 400 citations. Download: § gbif.org/science-review § gbif.org/science-review- sourcebook-2016 http://www.gbif.org/science-review dataaccessandus
- 20. GBIF Data examples of use
- 21. USING DATA THROUGH GBIF GBIF has established itself as an essential infrastructure underpinning science and policy related to biodiversity. Demonstrated by the growing volume of peer-reviewed research using data discovered and accessed through GBIF. Featured examples of use in Agriculture: http://www.gbif.org/newsroom/uses/ agriculture
- 30. Figure. The predicted distribu9on of 187 p r i o r i t y C W R i n Norway under the c u r r e n t c l i m a 9 c condi9ons. Red areas indicate taxon-rich areas with up to 124 taxa found there, and green areas indicate low taxon richness. Raster grid cell size 0.0416, approximately equal to 4 × 8 km2 CWR conservaAon Development of a conserva9on plan for Crop Wild Rela9ves in Norway extracted the CWR species occurrence data points from GBIF Phillips, J., Magos Brehm, J., van Oort, B. Asdal, Å., Rasmussen, M., Maxted, N. (2017) Climate change and na9onal crop wild rela9ve conserva9on planning. Ambio. DOI:10.1007/s13280-017-0905-y Phillips, J. Asdal, Å., Brehm, J.M., Morten Rasmussen M., Maxted, N. (2016) In situ and ex situ diversity analysis of priority crop wild rela9ves in Norway. Diversity and Distribu9ons, 22, 1112–1126. DOI: 10.1111/ddi.12470 Examples of use for GBIF-mediated data hrp://www.gbif.org/newsroom/uses/2016-phillips-et-al
- 48. Services to enable data analysis
- 49. GBIF DATA PORTAL API An interface to access data published through the GBIF network using web services.
- 50. ROPENSCI : RGBIF library(rgbif) key <- name_backbone(name='Hepatica nobilis', kingdom=‘Plantae')$speciesKey sp <- occ_search(taxonKey=key, return='data', hasCoordinate=TRUE, limit=1000) gbifmap(sp)
- 52. SCHOLARLY DATA CITATION IS GOOD RESEARCH PRACTICE • Data citation integrated part of the scholarly system • Supporting research validation and reproducibility • Enable reuse of research output and results • Tracking impact of published data • Scholarly structure to reward and credit people involved in producing research data
- 53. DOI – DIGITAL OBJECT IDENTIFIER Persistent resolvable identifiers Standard for scholarly journal papers Simplify citation of references Used for measuring impact
- 54. Data Publishers Any tool Publisher establishes DOI externally Any tool Publisher does not provide DOI Publisher uses IPT to register dataset with DataCite IPT Na9onal DataCite Service GBIF.org DataCite Denmark GBIF registers datasets without exis9ng DOIs with DataCite Denmark GBIF & DIGITAL OBJECT IDENTIFIERS (DOI) GBIF dataset DOI launced in September 2014: hrp://vimeo.com/107148220#t=6m28s
- 55. User searches for data through GBIF.org DataCite Denmark GBIF.org GBIF assigns DOIs to data downloads Cleaned data Data Data arribu9on Dataset DOI Researcher Paper Paper DOI User deposits cleaned dataset in a repository and gets DOI for dataset Published paper can give resolvable links to GBIF download and/ or to cleaned dataset User cleans data User publishes paper GBIF download Data Data arribu9on Download DOI Download history Download 1 . . . GBIF.org creates a download data set GBIF & DIGITAL OBJECT IDENTIFIERS (DOI) GBIF dataset DOI launced in September 2014: hrp://vimeo.com/107148220#t=6m28s
- 56. WHO HAS CITED YOUR DATA RESOURCE? CrossRef services link citations between scientific journal articles With CrossRef you can discover who has cited your research paper! Services to link dataset citations (DataCite DOI) with CrossRef systems Towards services in CrossRef to discover who cited your research data … hrp://blog.crossref.org/?s=DataCite
- 57. (...)
- 59. LICENSING FOR DATA PUBLISHED THROUGH GBIF http://www.gbif.org/terms/licences GBIF Governing Board established in 2014 support in GBIF for three licenses Status: set for all datasets published in GBIF since August 2016 GBIF Portal (status December 2016) CC0 57 % (409 million records) CC BY 4.0 30 % (215 million records) CC BY NC 4.0 13 % (93 million records)
- 60. DATA LICENSE REGULATES THE POSSIBILITY FOR REUSE OF DATA • CC0 data are made available for any use without restriction or particular requirements on the part of users. • CC BY data are made available for any use provided that attribution is appropriately given for the sources of data used. • CC NC data are made available for no-commercial use – however, how to limit what is considered to be "commercial use"? • CC SA data are made available provided conditional that derived products also are shared alike as CC SA – notice that this could block desired commercial products? • CC ND data are made available for verification read-only, however no modifications or derived products are allowed (blocking reuse)!
- 61. H2020 – OPEN DATA BY DEFAULT FROM 2017 Kilde: OpenAIRE & EUDAT, CC-BY-4.0, 2013
- 62. Darwin Core data exchange standard
- 64. Darwin Core – a vocabulary of terms Wieczorek J, Bloom D, Guralnick R, Blum S, Döring M, De Giovanni R, Robertson T, and Vieglais D (2012) Darwin Core: An Evolving Community-Developed Biodiversity Data Standard. PLoS ONE 7(1): e29715. (doi:10.1371/journal.pone.0029715)
- 66. MCPD (2012) Darwin Core MCPD (2012) Darwin Core (missing) dwc:datasetID 15.5 COORDUNCERT dwc:coordinateUncertaintyInMeters (missing) dwc:occurrenceID 15.6 COORDDATUM dwc:geode9c.Datum 1 INSTCODE dwc:ins9tu9onCode 15.7 GEOREFMETH dwc:georeferenceSources 2 ACCENUMB dwc:catalogNumber 16 ELEVATION dwc:minimumEleva9onInMeters 3 COLLNUMB dwc:recordNumber 17 COLLDATE dwc:eventDate 4 COLLCODE g:collec9ngIns9tuteCode 18 BREDCODE g:breederIns9tuteID 4.1 COLLNAME dwc:recordedBy 18.1 BREDNAME g:breedingIns9tute 4.1.1 COLLINSTADDRESS (dwc:recordedBy) 19 SAMPSTAT g:biologicalStatus 4.2 COLLMISSID dwc:collec9onCode 20 ANCEST g:ancestralData, g:purdyPedigree 5 GENUS dwc:genus 21 COLLSRC g:acquisi9onSource 6 SPECIES dwc:specificEpithet 22 DONORCODE g:donorIns9tuteID 7 SPAUTHOR dwc:scien9ficNameAuthorship 22.1 DONORNAME g:donorIns9tute 8 SUBTAXA dwc:infraspecificEpithet 23 DONORNUMB g:donorsIden9fier 9 SUBTAUTHOR (dwc:scien9ficNameAuthorship) 24 OTHERNUMB dwc:otherCatalogNumbers 10 CROPNAME dwc:vernacularName 25 DUPLSITE g:safetyDuplica9onIns9tuteID 11 ACCENAME g:breedingIden9fier 25.1 DUPLINSTNAME g:safetyDuplica9onIns9tute 12 ACQDATE g:acquisi9onDate 26 STORAGE g:storageCondi9on 13 ORIGCTY dwc:countryCode 27 MLSSTAT g:mlsStatus 14 COLLSITE dwc:locality 28 REMARKS dwc:occurrenceRemarks 15.1 DECLATITUDE dwc:decimalLa9tude 15.2 LATITUDE dwc:verba9mLa9tude 15.3 DECLONGITUDE dwc:decimalLongitude 15.4 LONGITUDE dwc:verba9mLongitude Mapping of DwC to to MCPD 66
- 67. Evaluation data
- 74. Publish your biodiversity data with GBIF
- 75. PUBLISH DATA IN GBIF datapublishing Step 1: data holding research institutes seek endorsement as an approved data publisher. Step 2: datasets are identified and converted to standard Darwin Core format. Step 3: datasets can be published directly from the data node and/or with the assistance from a national GBIF node (helpdesk). Citizen science data platforms also publish in GBIF.
- 76. WHAT IS DATA PUBLISHING? “Publishing” refers to making biodiversity datasets publicly accessible and discoverable, in a standardized form, via an access point, typically a web address (a URL). IPT
- 79. Persistent Identifiers Digital Object Identifiers (DOI)
- 80. The purpose of identifiers …is to name things, making it possible to refer to them.
- 84. DATA CITATION PRINCIPLES 1. Data to be legitimate citable products of research. 2. Data citations giving scholarly credit and attribution. 3. In scholarly literature, whenever claims are based on data, data should always be cited. 4. Persistent method for identification of data, that is machine actionable, globally unique, universal. 5. Data citation facilitate access to data or at least to metadata. 6. Unique identifiers that persist even beyond the lifespan of the data. 7. Data citation identify and access the specific data that support verification of the claim (provenance, time-slice, version). 8. Flexible, but attention to interoperability of practices across communities. Data Citation Synthesis Group: Joint Declaration of Data Citation Principles. Martone M. (ed.) San Diego CA: FORCE11; 2014
- 85. "FAIR" DATA Findable – assign persistent IDs, provide rich metadata, register in a searchable resource (such as GBIF) Accessible – Retrievable by their ID using a standard protocol, metadata remain accessible even if data aren’t Interoperable – Use formal, broadly applicable languages, use standard vocabularies, qualified references (e.g. Darwin Core) Reusable – Rich, accurate metadata, clear licences, provenance, use of community standards (e.g. Dublin Core, EML) www.force11.org/group/fairgroup/fairprinciples Slide source: OpenAIRE & EUDAT, CC-BY-4.0, 2013
- 86. GBIF news
- 87. LATEST NEWS 'Names in November' workshop targets single shared species list Partnership with taxonomic community aims for a single, sustainable information service for species names Read more 63.8 million new observations increase eBird total to 275 million records Annual dataset refresh grows by 30 per cent, with biggest gains in Asia and Europe Read more http://www.gbif.org/newsroom/summary Photo credits: (center) courtesy of Peter Schalk. (right) Abdomen of emerald ash borer (Argils planipennis) at 50x magnification by Macroscopic Solutions via Flickr. Photo licensed under CC BY-NC 2.0. communication Experts outline strategy for improving alien species information Task group recommends actions for reducing the impacts of invasive species on biodiversity Read more
- 88. LATEST NEWS First BID grants provide nearly €1 million in funding to 23 African projects ¤ EU-funded programme grantees represent 34 organizations from 20 African countries (Read more) ¤ Open call for Caribbean and the Pacific (read more) ¤ Read more about BID http://www.gbif.org/newsroom/summary Photos: (left) One Tree Plain, CC BY-NC-SA 2015 Geoff Livingston, (centre) Peacock pansy (Junonia almana), Ho Chi Minh, Vietnam. CC BY-SA 2015 Pavel Kirillov via iNaturalist. (right) Photo courtesy of Nestor Engone Obiang. communication BIFA grants to benefit 14 Asian countries Four project share €106,000 in funding to enhance data publishing capacity of current and future network members. Read more Belgium, Taiwan and Norway nodes provided BIFA funded mentoring for the AESEAN heritage parks in July 2016. Read more (at gbif.no) Appeal for help after damage Gabon's national herbarium Post-election riots in September spared collections, but caused major damage to the BID grantee’s headquarters in Libreville, Gabon. Read English or French
- 89. LATEST NEWS Four network projects awarded 2016 capacity enhancement support grants (mentoring) ¤ A total of €23,300 in funding will support the work of GBIF nodes and partners in five countries (Colombia, France, Guinea, Portugal, Spain). ¤ Read more http://www.gbif.org/newsroom/summary Photos:. (center) courtesy of GBIF Portugal. (right) Red-crested pochards (Netta rufina) off the eastern shore of Obersee, Switzerland, photo by roby 2016 CC BY-NC via iNaturalist. communication Four countries become the GBIF network’s newest national members ¤ Switzerland (voting) ¤ Ecuador (associate) ¤ Niger (associate) ¤ Nigeria (associate) New Darwin Core templates released Pre-configured Excel templates simplify data formatting, preparation and publication. – metadata template – checklist template – occurrence template – sampling event template Read more Template tool from GBIF.no
- 90. LATEST NEWS http://www.gbif.org/newsroom/summary Photos: (far right) © 2016 Williams Fagner. communication Data licensing milestone All species occurrence datasets on GBIF.org now carry standardized Creative Commons licenses. CC0 57 % CC-BY 4.0 30 % CC-BY-NC 4.0 13 % Read initial announcement and update 2016 Ebbe Nielsen Challenge winner Alejandro Ruete (Argentina, postdoc at SLU, Sweden) seeks to calculate ‘Where and when is there enough data?’ Read more 2016 Young Researchers Awards Meet the winners! – Mexican PhD student Juan M. Escamilla Mólgora – Brazilian Master’s student Bruno Umbelino